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Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax

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MaxUlysse 2020-02-24 14:37:27 +01:00
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2
.github/workflows/main.yml vendored
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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow - name: Install Nextflow

106
README.md
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@ -6,19 +6,19 @@ A repository for hosting Nextflow configuration files containing custom paramete
## Table of contents <!-- omit in toc --> ## Table of contents <!-- omit in toc -->
- [Using an existing config](#using-an-existing-config) * [Using an existing config](#using-an-existing-config)
- [Configuration and parameters](#configuration-and-parameters) * [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage) * [Offline usage](#offline-usage)
- [Adding a new config](#adding-a-new-config) * [Adding a new config](#adding-a-new-config)
- [Checking user hostnames](#checking-user-hostnames) * [Checking user hostnames](#checking-user-hostnames)
- [Testing](#testing) * [Testing](#testing)
- [Documentation](#documentation) * [Documentation](#documentation)
- [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
- [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
- [Pipeline-specific documentation](#pipeline-specific-documentation) * [Pipeline-specific documentation](#pipeline-specific-documentation)
- [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
- [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files) * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
- [Help](#help) * [Help](#help)
## Using an existing config ## Using an existing config
@ -93,30 +93,31 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems: Currently documentation is available for the following systems:
- [AWSBATCH](docs/awsbatch.md) * [AWSBATCH](docs/awsbatch.md)
- [BIGPURPLE](docs/bigpurple.md) * [BIGPURPLE](docs/bigpurple.md)
- [BINAC](docs/binac.md) * [BINAC](docs/binac.md)
- [CBE](docs/cbe.md) * [CBE](docs/cbe.md)
- [CCGA](docs/ccga.md) * [CCGA](docs/ccga.md)
- [CCGA_DX](/docs/ccga_dx.md) * [CCGA_DX](docs/ccga_dx.md)
- [CFC](docs/binac.md) * [CCGA_MED](docs/ccga_med.md)
- [CRICK](docs/crick.md) * [CFC](docs/binac.md)
- [CZBIOHUB_AWS](docs/czbiohub.md) * [CRICK](docs/crick.md)
- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) * [CZBIOHUB_AWS](docs/czbiohub.md)
- [DENBI_QBIC](docs/denbi_qbic.md) * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
- [GENOTOUL](docs/genotoul.md) * [DENBI_QBIC](docs/denbi_qbic.md)
- [GENOUEST](docs/genouest.md) * [GENOTOUL](docs/genotoul.md)
- [GIS](docs/gis.md) * [GENOUEST](docs/genouest.md)
- [HEBBE](docs/hebbe.md) * [GIS](docs/gis.md)
- [KRAKEN](docs/kraken.md) * [HEBBE](docs/hebbe.md)
- [MUNIN](docs/munin.md) * [KRAKEN](docs/kraken.md)
- [PASTEUR](docs/pasteur.md) * [MUNIN](docs/munin.md)
- [PHOENIX](docs/phoenix.md) * [PASTEUR](docs/pasteur.md)
- [PRINCE](docs/prince.md) * [PHOENIX](docs/phoenix.md)
- [SHH](docs/shh.md) * [PRINCE](docs/prince.md)
- [UCT_HEX](docs/uct_hex.md) * [SHH](docs/shh.md)
- [UPPMAX](docs/uppmax.md) * [UCT_HEX](docs/uct_hex.md)
- [UZH](docs/uzh.md) * [UPPMAX](docs/uppmax.md)
* [UZH](docs/uzh.md)
### Uploading to `nf-core/configs` ### Uploading to `nf-core/configs`
@ -125,7 +126,14 @@ Within the local clone of your fork add the custom config file to the [`conf/`](
You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that. In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error:
```bash
Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.
set(['<profile_name>'])
##[error]Process completed with exit code 1.
```
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information. Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
@ -153,13 +161,13 @@ Note that pipeline-specific configs are not required and should only be added if
Currently documentation is available for the following pipeline within the specific profile: Currently documentation is available for the following pipeline within the specific profile:
- ampliseq * ampliseq
- [BINAC](docs/pipeline/ampliseq/binac.md) * [BINAC](docs/pipeline/ampliseq/binac.md)
- sarek * eager
- [MUNIN](docs/pipeline/sarek/munin.md) * [SHH](docs/pipeline/eager/shh.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md) * sarek
- eager * [MUNIN](docs/pipeline/sarek/munin.md)
- [SHH](docs/pipeline/eager/shh.md) * [UPPMAX](docs/pipeline/sarek/uppmax.md)
### Enabling pipeline-specific configs within a pipeline ### Enabling pipeline-specific configs within a pipeline
@ -188,7 +196,7 @@ We will be notified automatically when you have created your pull request, and p
[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account. [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
And add or edit the following files in the local clone of your fork. And add or edit the following files in the local clone of your fork.
- `pipeline/<PIPELINE>.config` * `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -198,18 +206,18 @@ profiles {
} }
``` ```
- `conf/pipeline/<PIPELINE>/<PROFILE>.config` * `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory. Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<PIPELINE>.config` and set to reasonable values. Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<PIPELINE>.config` and set to reasonable values.
Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example. Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example.
- `docs/pipeline/<PIPELINE>/<PROFILE>.md` * `docs/pipeline/<PIPELINE>/<PROFILE>.md`
Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory. Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
- `README.md` * `README.md`
Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation

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4
conf/binac.config
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@ -13,14 +13,14 @@ singularity {
process { process {
beforeScript = 'module load devel/singularity/3.4.2' beforeScript = 'module load devel/singularity/3.4.2'
executor = 'pbs' executor = 'pbs'
queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'short' : 'long'} queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time > 48.h ? 'long' : 'short'}
} }
params { params {
igenomes_base = '/nfsmounts/igenomes' igenomes_base = '/nfsmounts/igenomes'
max_memory = 1000.GB max_memory = 1000.GB
max_cpus = 28 max_cpus = 28
max_time = 48.h max_time = 168.h
} }
weblog{ weblog{

39
conf/ccga_med.config Normal file
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@ -0,0 +1,39 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'CCGA Med cluster profile provided by nf-core/configs.'
config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
config_profile_url = 'https://www.ccga.uni-kiel.de/'
}
/*
* -------------------------------------------------
* Nextflow config file for CCGA cluster in Kiel
* -------------------------------------------------
*/
singularity {
enabled = true
runOptions = "-B /work_ifs -B /scratch"
cacheDir = "/work_ifs/ikmb_repository/singularity_cache/"
}
executor {
queueSize=100
}
process {
// Global process config
executor = 'slurm'
queue = 'all'
}
params {
// illumina iGenomes reference file paths on RZCluster
igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
saveReference = true
max_memory = 250.GB
max_cpus = 24
max_time = 120.h
}

16
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@ -0,0 +1,16 @@
# nf-core/configs: CCGA Med Cluster Configuration
Deployment and testing of nf-core pipelines at the CCGA Med cluster is on-going.
To use, run the pipeline with `-profile ccga_med`. This will download and launch the [`ccga_med.config`](../conf/ccga_med.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
```bash
## Load Nextflow and Singularity environment modules
module purge
module load nextflow
module load singularity
```
>NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner).

1
nfcore_custom.config
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@ -19,6 +19,7 @@ profiles {
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" } ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
crick { includeConfig "${params.custom_config_base}/conf/crick.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }